Probably because doing low level math is faster in C than in Java.
I was just wondering why would this user want to use a math engine written in C
as a rule of thumb that isn't the case, there are only 2 really important exceptions, SIMD and trigonometry(in some ranges) on x86 (trig on other platforms perform equally).
it is very important to always make a high level interface for the JNI code since the overhead of JNI is fairly high. (if you do single operations through JNI you will almost always lose performance)